Origin IGS: taaaaaaaaggttggttagacatactgcgactaaaaaaaggacgcgaggagcgcggggaggcgtttcaaaaaaacgtatctttgcgatgtggaattaaaaaacaacaggaacc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ggttcctgttgttttttaattccacatcgcaaagatacgtttttttgaaacgcctccccgcgctcctcgcgtcctttttttagtcgcagtatgtctaaccaacctttttttta Mask Tandem Repeat Region ================================================ taaaaaaaaggttggttagacatactgcgactaaaaaaaggacgcgaggagcgcggggaggcgtttcaaaaaaacgtatctttgcgatgtggaattaaaaaacaacaggaacc Find is-nt database================================================ Query_seq: TF0306:TF0307|TF0306:TF0307:transglutaminase-like enzyme/cysteine protease:conserved hypothetical protein:->->:332810..332922 113 taaaaaaaaggttggttagacatactgcgactaaaaaaaggacgcgaggagcgcggggaggcgtttcaaaaaaacgtatctttgcgatgtggaattaaaaaacaacaggaacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0306:TF0307|TF0306:TF0307:transglutaminase-like enzyme/cysteine protease:conserved hypothetical protein:->->:332810..332922 113 taaaaaaaaggttggttagacatactgcgactaaaaaaaggacgcgaggagcgcggggaggcgtttcaaaaaaacgtatctttgcgatgtggaattaaaaaacaacaggaacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0306:TF0307|TF0306:TF0307:transglutaminase-like enzyme/cysteine protease:conserved hypothetical protein:->->:332810..332922 113 taaaaaaaaggttggttagacatactgcgactaaaaaaaggacgcgaggagcgcggggaggcgtttcaaaaaaacgtatctttgcgatgtggaattaaaaaacaacaggaacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaaaaaaaggttggttagacatactgcgactaaaaaaaggacgcgaggagcgcggggaggcgtttcaaaaaaacgtatctttgcgatgtggaattaaaaaacaacaggaacc Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 22 End: 111 ..................... M L R L K K G R E E R G E A F Q K N V S L R C G I K K Q Q E .. taaaaaaaaggttggttagacatactgcgactaaaaaaaggacgcgaggagcgcggggaggcgtttcaaaaaaacgtatctttgcgatgtggaattaaaaaacaacaggaacc Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taaaaaaaaggttggttagacatactgcgactaaaaaaaggacgcgaggagcgcggggaggcgtttcaaaaaaacgtatctttgcgatgtggaattaaaaaacaacaggaacc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 50 HP_score: -2.7 Tail_Score: -3.63805 Start: 58 End: 80 Full_Region: CGCGAGGAGCGCGGG GAGGCGTTT CAAAA AAACGTATC TTTGCGATGTGGAAT .........................................................GAGGCGTTTCAAAAAAACGTATC................................. Find igs database================================================ Query_seq: TF0306:TF0307|TF0306:TF0307:transglutaminase-like enzyme/cysteine protease:conserved hypothetical protein:->->:332810..332922 113 taaaaaaaaggttggttagacatactgcgactaaaaaaaggacgcgaggagcgcggggaggcgtttcaaaaaaacgtatctttgcgatgtggaattaaaaaacaacaggaacc Intra-Species Hit: Count: 1 Min: 10 Max: 113 Len: 104 Subject: tfor_TF0306_TF0307|transglutaminase-like enzyme/cysteine protease:conserved hypothetical protein|POSITIVE:POSITIVE|[332810,332922]|113 HSP 1 e-value: 1.0E-27 bit: 123.0 Len: 104 Query Start:10 Query End:113 Subject Strand: POSITIVE Subject Start: 10 Subject End: 113 .........ggttggttagacatactgcgactnnnnnnnggacgcgaggagcgcggggaggcgtttcnnnnnnncgtatctttgcgatgtggaattaaaaaacaacaggaacc .........ggttggttagacatactgcgactaaaaaaaggacgcgaggagcgcggggaggcgtttcaaaaaaacgtatctttgcgatgtggaattaaaaaacaacaggaacc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGUUGGUUAGACAUACUGCGACUAAAAAAAGGACGCGAGGAGCGCGGGGAGGCGUUUCAAAAAAACGUAUCUUUGCGAUGUGGAAUUAAAAAACAACAGGAACC .((((.((((.((((..(((.((......))..)))......((((((((.((((((.....)))))).)))))))).))))...))))....))))....... (-25.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGUUCCUGUUGUUUUUUAAUUCCACAUCGCAAAGAUACGUUUUUUUGAAACGCCUCCCCGCGCUCCUCGCGUCCUUUUUUUAGUCGCAGUAUGUCUAACCAACC ((((.......................(((...((..((((((...))))))..))...)))......(((..((......)).))).........)))).... (-13.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 479 77 35 189 138 tfor:TF2127|5end_hypothetical_protein_2304038..2304268_POSITIVE 448 60 17 171 119 tfor:TF1624|5end_carboxyl-terminal_protease_1737252..1737482_POSITIVE 392 85 44 113 69 tfor:TF0019|5end_heat_shock_protein_ClpB_12450..12680_POSITIVE 386 50 10 58 14 tfor:TF2509|5end_ATP-dependent_clp_protease,_proteolytic_subunit_2687562..2687792_POSITIVE 385 55 14 51 5 tfor:TF0416|5end_possible_ATP-binding_protein_433134..433364_POSITIVE 383 78 31 124 71 tfor:TF2917|5end_conserved_hypothetical_protein_3112255..3112485_POSITIVE 348 59 31 62 28 tfor:TF2273|5end_conserved_hypothetical_protein_2436398..2436628_POSITIVE 342 80 31 209 161 tfor:TF1431|5end_conserved_hypothetical_protein;_possible_acyltransferase_1515104..1515334_POSITIVE 341 78 37 228 181 tfor:TF0874|5end_transposase_925685..925915_POSITIVE 340 49 2 155 107 tfor:TF1182|5end_hypothetical_protein_1268565..1268795_POSITIVE 338 58 12 54 3 tfor:TF3105|5end_hypothetical_protein_3338068..3338298_POSITIVE 336 78 31 78 5 tfor:TF1237|5end_possible_L-fuculose_kinase_1322041..1322271_POSITIVE 335 86 42 92 36 tfor:TF0688|5end_membrane-associated_protein,_possible_sulfatase_family_732760..732990_POSITIVE 335 80 32 62 19 tfor:TF0027|5end_conserved_hypothetical_protein_22866..23096_POSITIVE 334 69 30 93 42 tfor:TF2513|5end_conserved_hypothetical_protein_2691146..2691376_POSITIVE 333 70 29 85 43 tfor:TF1449|5end_RNA_polymerase_sigma_factor,_RpoD_1533124..1533354_POSITIVE 333 77 32 193 144 tfor:TF0234|5end_5,10-methylenetetrahydrofolate_reductase_260482..260712_POSITIVE 333 50 4 90 39 tfor:TF0015|5end_outer_membrane_protein_(possible_immunogenic_lipoprotein)_9555..9785_POSITIVE 332 78 32 52 4 tfor:TF1662|5end_possible_transcriptional_regulator,_PadR_family_1777214..1777444_POSITIVE 329 77 31 187 139 tfor:TF2014|5end_dipeptidyl_aminopeptidase_IV_2169398..2169628_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 479 77 35 67 16 tfor:TF2126|3end_S-adenosylhomocysteine_hydrolase_2303996..2304146_POSITIVE 363 54 16 41 1 tfor:TF2508|3end_ATP-dependent_Clp_protease,_ATP-binding_subunit_clpX_2687621..2687771_POSITIVE 351 77 31 86 23 tfor:TF1167|3end_hypothetical_protein_1248932..1249082_POSITIVE 351 76 35 70 12 tfor:TF0525|3end_conserved_hypothetical_protein_549584..549734_POSITIVE 348 59 31 98 64 tfor:TF2272|3end_conserved_hypothetical_protein_2436514..2436664_POSITIVE 334 69 30 69 18 tfor:TF2512|3end_possible_abortive_infection_protein_2691202..2691352_POSITIVE 329 77 31 50 2 tfor:TF2013|3end_polysaccharide_deacetylase_2169341..2169491_POSITIVE 329 45 1 146 105 tfor:TF0251|3end_conserved_hypothetical_protein;_possible_exporter_283529..283679_POSITIVE 326 85 42 86 37 tfor:TF2673|3end_conserved_hypothetical_protein_2848272..2848422_POSITIVE 314 80 34 148 111 tfor:TF2529|3end_nucleotidyl_transferase_family;_possible_mannose-1-phosphate_guanyltransferase_2711496..2711646_POSITIVE 314 80 31 93 44 tfor:TF2331|3end_conserved_hypothetical_protein_2491767..2491917_POSITIVE 313 59 11 85 20 tfor:TF0984|3end_possible_mucin-desulfating_sulfatase_(MdsC_protein)_1041424..1041574_POSITIVE 311 78 35 97 36 tfor:TF2018|3end_hypothetical_protein_2175315..2175465_POSITIVE 311 80 34 54 8 tfor:TF0250|3end_glycosyltransferase_Family_2_protein_280035..280185_POSITIVE 309 56 12 128 82 tfor:TF1850|3end_Na+/H+-exchanging_protein_2000913..2001063_POSITIVE 306 76 31 94 39 tfor:TF2007|3end_uracil_phosphoribosyltransferase_2159327..2159477_POSITIVE 306 68 31 99 65 tfor:TF1919|3end_hypothetical_protein_2070383..2070533_POSITIVE 306 80 31 59 17 tfor:TF1421|3end_UDP-N-acetylmuramate--alanine_ligase_1504921..1505071_POSITIVE 306 78 34 63 5 tfor:TF1236|3end_L-rhamnose_isomerase_1322106..1322256_POSITIVE 302 79 33 94 39 tfor:TF2726|3end_outer_membrane_protein,_possibly_involved_in_nutrient_binding_2903302..2903452_POSITIVE